Fix test-dimensionReduction, now passing

compbiomed · Jan 19, 2024 · 3f86b06 · 3f86b06
1 parent 17ad581
commit 3f86b06
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Showing 9 changed files with 7 additions and 7 deletions.
diff --git a/R/getTopHVG.R b/R/getTopHVG.R
@@ -111,7 +111,7 @@ setTopHVG <- function(inSCE,
         }
     } else {
         # Use pre-calculated variability metrics
-        features <- getTopHVG(inSCE, method = method, hvgNumber = hvgNumber,
+        features <- getTopHVG(inSCE, method = method, hvgNumber = hvgNumber,useFeatureSubset = NULL,
                               featureDisplay = NULL)
         useAssay <- metadata(inSCE)$sctk$runFeatureSelection[[method]]$useAssay
     }

diff --git a/R/importGeneSets.R b/R/importGeneSets.R
@@ -357,7 +357,7 @@ importGeneSetsFromCollection <- function(inSCE, geneSetCollection,
 #'                                 by = "feature_name")
 #' @export
 #' @importFrom SummarizedExperiment rowData
-importGeneSetsFromMSigDB <- function(inSCE, categoryIDs,
+importGeneSetsFromMSigDB <- function(inSCE, categoryIDs = "H",
                                      species = "Homo sapiens",
                                      mapping = c("gene_symbol",
                                             "human_gene_symbol",

diff --git a/R/plotPCA.R b/R/plotPCA.R
@@ -24,7 +24,7 @@ plotPCA <- function(inSCE, colorBy=NULL, shape=NULL, pcX="PC1",
   if(!(reducedDimName %in% names(SingleCellExperiment::reducedDims(inSCE)))){
     if (runPCA){
       inSCE <- scaterPCA(inSCE, useAssay = useAssay,
-                      reducedDimName = reducedDimName)
+                      reducedDimName = reducedDimName, useFeatureSubset = NULL)
     } else {
       stop(reducedDimName,
            " dimension not found. Run scaterPCA() or set runPCA to TRUE.")

diff --git a/R/runFeatureSelection.R b/R/runFeatureSelection.R
@@ -27,8 +27,8 @@
 #'                                            "modelGeneVar")
 runFeatureSelection <- function(inSCE,
                                 useAssay,
-                                method = c("vst", "mean.var.plot",
-                                           "dispersion", "modelGeneVar", "cell_ranger")){
+                                method = "modelGeneVar")
+  {
   method <- match.arg(method)
   seuratMethods <- c("vst", "mean.var.plot", "dispersion")
   scranMethods <- c("modelGeneVar")

diff --git a/R/runVAM.R b/R/runVAM.R
@@ -47,7 +47,7 @@
 #' sce <- runVAM(inSCE = sce,
 #'               geneSetCollectionName = "GeneSetCollection",
 #'               useAssay = "logcounts")
-runVAM <- function(inSCE, geneSetCollectionName, useAssay,
+runVAM <- function(inSCE, geneSetCollectionName = "H", useAssay = "logcounts",
                    resultNamePrefix = NULL, center = FALSE, gamma = TRUE) {
   ###################################################
   ###  create gene set collection

diff --git a/tests/testthat/SCE_cellData.txt.gz b/tests/testthat/SCE_cellData.txt.gz
diff --git a/tests/testthat/SCE_featureData.txt.gz b/tests/testthat/SCE_featureData.txt.gz
diff --git a/tests/testthat/assays/SCE_counts.mtx.gz b/tests/testthat/assays/SCE_counts.mtx.gz
diff --git a/tests/testthat/test-dimensionReduction.R b/tests/testthat/test-dimensionReduction.R
@@ -15,7 +15,7 @@ test_that(desc = "Testing scaterPCA", {
     testthat::expect_true("PCA1" %in% reducedDimNames(sce))
 
     sce <- scaterPCA(sce, useAssay = "hvgAltExplogcounts", useAltExp = "hvgAltExp",
-                     reducedDimName = "PCA2")
+                     useFeatureSubset = NULL, reducedDimName = "PCA2")
     testthat::expect_true("PCA2" %in% reducedDimNames(sce))
 
     expect_error({